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Micro-RNAs (miRNAs): genomic organisation, biogenesis and mode of action

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Abstract

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression in animals and in plants. In recent years, miRNAs have been shown to be important biological molecules for regulating various cellular functions. miRNAs function post-transcriptionally usually by base-pairing to the mRNA 3′-untranslated regions of the mRNAs and repress protein synthesis by mechanisms that are not fully understood. Various miRNA genes have been mapped in the genome of a number of organisms and the list continues to grow. Details regarding the genomic organisation, transcriptional regulation and post-transcriptional maturation of miRNAs are still emerging. In this review, information regarding the genomic organisation, biogenesis and regulation of expression of miRNAs is discussed.

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Abbreviations

miRNA:

Micro-RNA

Pri-miRNA:

Primary miRNA

Pre-miRNA:

Precursor miRNA

miRISC:

miRNA-inducing silencing complex

RNAi:

RNA interference

AGO:

Argonaute family protein

GW182:

Glycine-tryptophan (GW) repeat-containing protein of 182 kDa

PABP:

Poly(A)-binding protein

CCR4-CAF1-NOT1:

Deadenylase complex

References

  • Ameres SL, Martinez J, Schroeder R (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130:101–112

    Article  PubMed  CAS  Google Scholar 

  • Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R (2008) Mouse ES cells express endogenous shRNAs, siRNAs, and other microprocessor-independent. Dicer dependent small RNAs. Genes Dev 22:2773–2785

    Article  PubMed  CAS  Google Scholar 

  • Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122:553–563

    Article  PubMed  CAS  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  PubMed  CAS  Google Scholar 

  • Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

    Article  PubMed  CAS  Google Scholar 

  • Baskerville S, Bartel DP (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11:241–247

    Article  PubMed  CAS  Google Scholar 

  • Basyuk E, Suavet F, Doglio A, Bordonne R, Bertrand E (2003) Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res 31:6593–6597

    Article  PubMed  CAS  Google Scholar 

  • Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E (2006) mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev 20:1885–1898

    Article  PubMed  CAS  Google Scholar 

  • Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363–366

    Article  PubMed  CAS  Google Scholar 

  • Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3:e85

    Article  PubMed  Google Scholar 

  • Bushati N, Cohen SM (2007) MicroRNA functions. Annu Rev Cell Dev Biol 23:175–205

    Article  PubMed  CAS  Google Scholar 

  • Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10:1957–1966

    Article  PubMed  CAS  Google Scholar 

  • Chang TC, Yu D, Lee YS, Wentzel EA, Arking DE, West KM, Dang CV, Thomas-Tikhonenko A et al (2008) Widespread microRNA repression by Myc contributes to tumorigenesis. Nat Genet 40:43–50

    Article  PubMed  CAS  Google Scholar 

  • Chekulaeva M, Filipowicz W (2009) Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Curr Opin Cell Biol 21:452–460

    Article  PubMed  CAS  Google Scholar 

  • Chendrimada TP, Finn KJ, Ji X, Baillat D, Gregory RI, Liebhaber SA, Pasquinelli AE, Shiekhattar R (2007) MicroRNA silencing through RISC recruitment of eIF6. Nature 447:823–828

    Article  PubMed  CAS  Google Scholar 

  • Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC (2011) Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res 21:286–300

    Article  PubMed  CAS  Google Scholar 

  • Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One 4:e5279

    Article  PubMed  Google Scholar 

  • Davis-Dusenbery BN, Hata A (2010) MicroRNA in cancer. The involvement of aberrant microRNA biogenesis regulatory pathway. Genes Cancer 1:1100–1114

    Article  PubMed  CAS  Google Scholar 

  • Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ (2004) Processing of primary microRNAs by the microprocessor complex. Nature 432:231–235

    Article  PubMed  CAS  Google Scholar 

  • Ender C, Krek A, Friedländer M, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N et al (2008) A human snoRNA with microRNA-like functions. Mol Cell 32:519–528

    Article  PubMed  CAS  Google Scholar 

  • Eulalio A, Huntzinger E, Izaurralde E (2008) Getting to the root of miRNA-mediated gene silencing. Cell 132:9–14

    Article  PubMed  CAS  Google Scholar 

  • Eulalio A, Huntzinger E, Nishihara T, Rehwinkel J, Fauser M, Izaurralde E (2009) Deadenylation is a widespread effect of miRNA regulation. RNA 15:21–32

    Article  PubMed  CAS  Google Scholar 

  • Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M et al (2009) Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell 35:868–880

    Article  PubMed  CAS  Google Scholar 

  • Fabian MR, Sonenberg N, Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79:351–379

    Article  PubMed  CAS  Google Scholar 

  • Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9:102–114

    Article  PubMed  CAS  Google Scholar 

  • Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105

    Article  PubMed  CAS  Google Scholar 

  • Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108

    Article  PubMed  CAS  Google Scholar 

  • Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312:75–79

    Article  PubMed  CAS  Google Scholar 

  • Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R (2004) The microprocessor complex mediates the genesis of microRNAs. Nature 432:235–240

    Article  PubMed  CAS  Google Scholar 

  • Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004) The Drosha–DGCR8 complex in primary microRNA processing. Genes Dev 18:3016–3027

    Article  PubMed  CAS  Google Scholar 

  • Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y et al (2006) Molecular basis for the recognition of primary microRNAs by the Drosha–DGCR8 complex. Cell 125:887–901

    Article  PubMed  CAS  Google Scholar 

  • Henke JI, Goergen D, Zheng J, Song Y, Schüttler CG, Fehr C, Jünemann C, Niepmann M (2008) microRNA-122 stimulates translation of hepatitis C virus RNA. EMBO J 27:3300–3310

    Article  PubMed  CAS  Google Scholar 

  • Humphreys DT, Westman BJ, Martin DI, Preiss T (2005) MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc Natl Acad Sci USA 102:16961–16966

    Article  PubMed  CAS  Google Scholar 

  • Huntzinger E, Izaurralde E (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12:99–110

    Article  PubMed  CAS  Google Scholar 

  • Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293:834–838

    Article  PubMed  CAS  Google Scholar 

  • Jinek M, Doudna JA (2009) A three-dimensional view of the molecular machinery of RNA interference. Nature 457:405–412

    Article  PubMed  CAS  Google Scholar 

  • Jopling CL, Schutz S, Sarnow P (2008) Position-dependent function for a tandem microRNA miR-122-binding site located in the hepatitis C virus RNA genome. Cell Host Microbe 4:77–85

    Article  PubMed  CAS  Google Scholar 

  • Kawamata T, Tomari Y (2010) Making RISC. Trends Biochem Sci 35:368–376

    Article  PubMed  CAS  Google Scholar 

  • Kim YK, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26:775–783

    Article  PubMed  CAS  Google Scholar 

  • Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA 101:360–365

    Article  PubMed  CAS  Google Scholar 

  • Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858

    Article  PubMed  CAS  Google Scholar 

  • Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T (2003) New microRNAs from mouse and human. RNA 9:175–179

    Article  PubMed  CAS  Google Scholar 

  • Lanet E, Delannoy E, Sormani R, Floris M, Brodersen P, Crété P, Voinnet O, Robaglia C (2009) Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 21:1762–1768

    Article  PubMed  CAS  Google Scholar 

  • Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862

    Article  PubMed  CAS  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854

    Article  PubMed  CAS  Google Scholar 

  • Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21:4663–4670

    Article  PubMed  CAS  Google Scholar 

  • Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P et al (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415–419

    Article  PubMed  CAS  Google Scholar 

  • Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23:4051–4060

    Article  PubMed  CAS  Google Scholar 

  • Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L et al (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305:1437–1441

    Article  PubMed  CAS  Google Scholar 

  • Lujambio A, Esteller M (2009) How epigenetics can explain human metastasis: a new role for microRNAs. Cell Cycle 8:377–382

    Article  PubMed  CAS  Google Scholar 

  • Lujambio A, Calin GA, Villanueva A, Ropero S, Sánchez-Céspedes M, Blanco D, Montuenga LM, Rossi S et al (2008) A microRNA DNA methylation signature for human cancer metastasis. Proc Natl Acad Sci USA 105:13556–13561

    Article  PubMed  CAS  Google Scholar 

  • Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303:95–98

    Article  PubMed  CAS  Google Scholar 

  • MacRae IJ, Doudna JA (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol 17:138–145

    Article  PubMed  CAS  Google Scholar 

  • Maroney PA, Yu Y, Fisher J, Nilsen TW (2006) Evidence that microRNAs are associated with translating messenger RNAs in human cells. Nat Struct Mol Biol 13:1102–1107

    Article  PubMed  CAS  Google Scholar 

  • Mathonnet G, Fabian MR, Svitkin YV, Parsyan A, Huck L, Murata T, Biffo S, Merrick WC et al (2007) MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317:1764–1767

    Article  PubMed  CAS  Google Scholar 

  • Meltzer PS (2005) Small RNAs with big impacts. Nature 435:740–746

    Article  Google Scholar 

  • Morlando M, Ballarino M, Gromak N, Pagano F, Bozzoni I, Proudfoot NJ (2008) Primary microRNA transcripts are processed co-transcriptionally. Nat Struct Mol Biol 15:902–909

    Article  PubMed  CAS  Google Scholar 

  • Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M et al (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16:720–728

    Article  PubMed  CAS  Google Scholar 

  • Nasser MW, Datta J, Nuovo G, Kutay H, Motiwala T, Majumder S, Wang B, Suster S et al (2008) Down-regulation of micro-RNA-1 (miR-1) in lung cancer suppression of tumorigenic property of lung cancer cells and their sensitization to doxorubicin-induced apoptosis by miR-1. J Biol Chem 283:33394–33405

    Article  PubMed  CAS  Google Scholar 

  • Nottrott S, Simard MJ, Richter JD (2006) Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nat Struct Mol Biol 13:1108–1114

    Article  PubMed  CAS  Google Scholar 

  • Okamura K, Hagen JW, Duan H, Tyler DM, Lai E (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130:89–100

    Article  PubMed  CAS  Google Scholar 

  • Orom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 5′UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30:460–471

    Article  PubMed  Google Scholar 

  • Ota A, Tagawa H, Karnan S, Tsuzuki S, Karpas A, Kira S, Yoshida Y, Seto M (2004) Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res 64:3087–3095

    Article  PubMed  CAS  Google Scholar 

  • Peters L, Meister G (2007) Argonaute proteins: mediators of RNA silencing. Mol Cell 26:611–623

    Article  PubMed  CAS  Google Scholar 

  • Petersen CP, Bordeleau ME, Pelletier J, Sharp PA (2006) Short RNAs repress translation after initiation in mammalian cells. Mol Cell 21:533–542

    Article  PubMed  CAS  Google Scholar 

  • Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E, Filipowicz W (2005) Inhibition of translational initiation by let-7 microRNA in human cells. Science 309:1573–1576

    Article  PubMed  CAS  Google Scholar 

  • Rehwinkel J, Behm-Ansmant I, Gatfield D, Izaurralde E (2005) A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA 11:1640–1647

    Article  PubMed  CAS  Google Scholar 

  • Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901–906

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14:1902–1910

    Article  PubMed  CAS  Google Scholar 

  • Ruby JG, Jan CH, Bartel DP (2007) Intronic microRNA precursors that bypass Drosha processing. Nature 448:83–86

    Article  PubMed  CAS  Google Scholar 

  • Saini HK, Griffiths-Jones S, Enright AJ (2007) Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci USA 104:17719–17724

    Article  PubMed  CAS  Google Scholar 

  • Saito Y, Liang G, Egger G, Friedman JM, Chuang JC, Coetzee GA, Jones PA (2006) Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 9:435–443

    Article  PubMed  CAS  Google Scholar 

  • Schwer B (2003) A new twist on RNA helicases: DExH/D box proteins as RNPases. Nat Struct Biol 8:113–116

    Article  Google Scholar 

  • Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, Martienssen RA, Hannon GJ, Joshua-Tor L (2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol 10:1026–1032

    Article  PubMed  CAS  Google Scholar 

  • Suzuki HI, Yamagata K, Sugimoto K, Iwamoto T, Kato S, Miyazono K (2009) Modulation of microRNA processing by p53. Nature 460:529–533

    Article  PubMed  CAS  Google Scholar 

  • Tagawa H, Karube K, Tsuzuki S, Ohshima K, Seto M (2007) Synergistic action of the microRNA-17 polycistron and Myc in aggressive cancer development. Cancer Sci 98:1482–1490

    Article  PubMed  CAS  Google Scholar 

  • Tarun SZ Jr, Wells SE, Deardorff JA, Sachs AB (1997) Translation initiation factor eIF4G mediates in vitro poly(A) tail-dependent translation. Proc Natl Acad Sci USA 94:9046–9051

    Article  PubMed  CAS  Google Scholar 

  • Thermann R, Hentze MW (2007) Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447:875–878

    Article  PubMed  CAS  Google Scholar 

  • Vasudevan S, Steitz JA (2007) AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 128:1105–1118

    Article  PubMed  CAS  Google Scholar 

  • Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can upregulate translation. Science 318:1931–1934

    Article  PubMed  CAS  Google Scholar 

  • Wakiyama M, Takimoto K, Ohara O, Yokoyama S (2007) Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev 21:1857–1862

    Article  PubMed  CAS  Google Scholar 

  • Warf MB, Johnson WE, Bass BL (2011) Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. RNA 17:563–577

    Article  PubMed  CAS  Google Scholar 

  • Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75:855–862

    Article  PubMed  CAS  Google Scholar 

  • Wu L, Fan J, Belasco JG (2006) MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci USA 103:4034–4039

    Article  PubMed  CAS  Google Scholar 

  • Yi R, Qin Y, Macara IG, Cullen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17:3011–3016

    Article  PubMed  CAS  Google Scholar 

  • Zekri L, Huntzinger E, Heimstädt S, Izaurralde E (2009) The silencing domain of GW182 interacts with PABPC1 to promote translational repression and degradation of miRNA targets and is required for target release. Mol Cell Biol 29:6220–6231

    Article  PubMed  CAS  Google Scholar 

  • Zeng Y, Cullen BR (2004) Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res 32:4776–4785

    Article  PubMed  CAS  Google Scholar 

  • Zeng Y, Cullen BR (2005) Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J Biol Chem 280:27595–27603

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Mahboob Ul Hussain.

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Financial support to M.U.H. from the Department of Biotechnology (BT/PR11917/Med/30/181/2009), New Delhi is acknowledged.

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Hussain, M.U. Micro-RNAs (miRNAs): genomic organisation, biogenesis and mode of action. Cell Tissue Res 349, 405–413 (2012). https://doi.org/10.1007/s00441-012-1438-0

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